5DR2

Aurora A Kinase in Complex with AA30 and ATP in Space Group P6122


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4292100 mM HEPES pH 7.4, 200 mM magnesium sulphate, 2-20 PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5852.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.26α = 90
b = 83.26β = 90
c = 163.85γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9184DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.4672.111000.08618.718.11289884.34
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.462.521002.1491.619

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3FDN2.4672.111217966799.980.22460.221330.28495RANDOM80.765
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.05-0.03-0.050.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.606
r_dihedral_angle_4_deg20.891
r_dihedral_angle_3_deg19.264
r_long_range_B_refined12.739
r_long_range_B_other12.739
r_scangle_other9.913
r_mcangle_it9.174
r_mcangle_other9.17
r_scbond_it7.787
r_scbond_other7.785
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.606
r_dihedral_angle_4_deg20.891
r_dihedral_angle_3_deg19.264
r_long_range_B_refined12.739
r_long_range_B_other12.739
r_scangle_other9.913
r_mcangle_it9.174
r_mcangle_other9.17
r_scbond_it7.787
r_scbond_other7.785
r_mcbond_it7.69
r_mcbond_other7.689
r_dihedral_angle_1_deg5.872
r_angle_refined_deg1.903
r_angle_other_deg1.114
r_chiral_restr0.105
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2162
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing
XDSdata reduction
Aimlessdata scaling